Issues with using alternative taxonomy in command line of Linux

I’m currently attempting to annotate and classify my gene sequence (CuMMO) using the lowest common ancestor algorithm and the results from BlastN through MEGAN.

I have prepared the necessary files for the alternative taxonomy (file of .tre and .map), and have successfully run it through the graphical interface on my macOS system.

However, I need to perform batch operations, so I tried running MEGAN on the Linux command line, during which I can’t seem to find the parameters for the alternative taxonomy in blast2lca. Do I need to use another plugin to replicate a similar process in MEGAN6? Thanks a lot for your attention and assistance :smiling_face_with_three_hearts:!

There is currently no commandline options to set the alternative taxonomy. However, the commandline programs all use the same preferences file as MEGAN, and so if you ran MEGAN on the same user account and computer and set an alternative taxonomy in MEGAN during that run, then the commandline tools should all use the alternative taxonomy.

More explicitly, adding a line like the following to the ~/.Megan.def properties file should result in blast2lca loading the alternative taxonomy:

TaxonomyFile= <path-to-alternative-tre-file>